The study presents the development of a biosafety system in aquaculture activities on the territory of the Murmansk region, accounting for the existing scientific developments and recommendations. The authors’ scientific and practical experience in cultivating the hydrobionts in the conditions of the Polar region is the core of the study. The materials for the development of the regional biosafety program of salmon cages farms were the longstanding epizootic and ichthiopathological studies of the department of fish physiology and diseases, aquaculture objects of the Murmansk Regional Animal Disease Control Center (2013–2019). The most significant risks for salmon net farms of the Murmansk region are: carrying out activities in the zone of risky fish farming; lack (or scarcity) of high-quality nursery material of domestic origin, absence of the center for research and prevention of fish diseases; the absence of the specialized enterprise for aquaculture waste disposal. The developed system of practical safety of aquaculture enterprises in the region will allow managing the risks through certain efforts and events. The principles of biosafety system development in accordance with the environmental requirements and associated conditions for maintaining the epizootic and ichthyopathological safety in the commercial cultivation of fish are considered. Preventive measures to maintain epizootic safety in fish farms have been developed. Suggestions and recommendations are formulated to conduct safe aquaculture activities in the conditions of the Murmansk region. A integrated approach to biosafety through certain risk management activities is aimed at solving the problems of preserving the health of cultivated objects resulting in the maximal feasibility of the enterprise and maintaining the biodiversity of natural communities and environmental sustainability in the region.